I had that problem for a while, I used the average. I had 3-4 players so that was convenient for me. don't know if that is doable for a 3-6 group.
Another solution could be to use a factor of 6 (your maximum number of players) and when you have a for example four players, you as a GM spend 2 WP somewhere where you think is appropriate. Normally you do this if there are no players in the Ark and no Assembly and so on, but in those cases you spend WP equal to the number of players. But using this method you spend WP equal to the number of players that doesn't participate in this session. This way is also good because you (GM) can spend WP on things that is logically should happen/be in the Ark, but that the players haven't chosen.
“I’d say thistles, but nobody listens to me, anyway.” - Eeyore